From chemistry-request@server.ccl.net Tue Aug 14 07:51:41 2001 Received: from rudjer.irb.hr (dbabic@[161.53.128.19]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7EBpdv07877 for ; Tue, 14 Aug 2001 07:51:39 -0400 Received: from localhost (dbabic@localhost) by rudjer.irb.hr (8.10.0/8.10.0VS) with ESMTP id f7EBp6E28782; Tue, 14 Aug 2001 13:51:07 +0200 (MET DST) Date: Tue, 14 Aug 2001 13:51:05 +0200 (MET DST) From: Darko Babic To: Zhenhua Li cc: CCL Subject: Re: CCL:g98 error on linux In-Reply-To: <006e01c123f3$eace53a0$c40b140a@lizhenhua> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I met this too. Look into the installation log file (if you have one) and you'll find that the linker complains about referring to the obsolete tmpnam (or something) functions. There were two library files referring to this (or similar) functions: the blas-f2c.a (co- ming with the optimized BLAS libraries) and one of the PGI libraries. The solution was to give up of optimized BLAS (I couldn't find some other version of blas-f2c library or its source) and to upgrade com- piler. Check which of these two libraries you have and replace them or leave out. If not possible, use the binary version from RedHat 6.2. There was another problem after that: SMP jobs occasionally died for no obvious reason. After recompilation with libpgthread.so instead of libpthread.so, the program became stable. I'm afraid this might happen with the binary version from RedHat 6.2, but I'm not sure. If you need more details, let me know. Darko Darko Babic Institute "Rudjer Boskovic" HR-10002 Zagreb, P.O.B. 180 Croatia -------------------------------------------------------------------- On Mon, 13 Aug 2001, Zhenhua Li wrote: > Dear CCLers, > When I ran g98 in Linux Redhat 7.1. But following error appeared: > g98: error while loading shared libraries: /home/scratch/test/g98/util.so: > undefined symbol: fstat > Nothing appeared in output file at all. > > I can't find out what's wrong with it. Can anyone help me? > Thanks in advance. > > Li Zhenhua > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Tue Aug 14 08:23:35 2001 Received: from baton.phys.lsu.edu ([130.39.182.71]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7ECNZv08337 for ; Tue, 14 Aug 2001 08:23:35 -0400 Received: (from vani@localhost) by baton.phys.lsu.edu (8.9.2/8.9.2) id HAA28978; Tue, 14 Aug 2001 07:20:25 -0500 (CDT) Date: Tue, 14 Aug 2001 07:20:22 -0500 (CDT) From: Vemparala Satyavani To: chemistry@ccl.net Subject: initial configuration of PMMA(or any polymer) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, while preparing the inital configuration of polymers i make a single chain with the bond length and bond angle specifications and then apply 'pivot Monte carlo'. The problem, is making that single chain sometimes takes a long time, and especially in polymers like PMMA with long side chains. Is there a code anywhere/an easier method to make the initial chain? Thanks vani From chemistry-request@server.ccl.net Tue Aug 14 09:39:22 2001 Received: from zcsn04.astrazeneca.com ([193.128.1.35]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7EDdMv09899 for ; Tue, 14 Aug 2001 09:39:22 -0400 Received: from zcsn14.ukhx.astrazeneca.net (zcsn14.ukhx.astrazeneca.net [192.168.199.14]) by zcsn04.astrazeneca.com (8.9.3/8.9.3.DEF) with ESMTP id OAA02123 for ; Tue, 14 Aug 2001 14:39:20 +0100 (BST) From: parthiban.srinivasan@astrazeneca.com Received: from sesosn21.seso.astrazeneca.net (sesosn21.seso.astrazeneca.net [192.71.145.181]) by zcsn14.ukhx.astrazeneca.net (8.9.3/8.9.3) with ESMTP id NAA09130 for ; Tue, 14 Aug 2001 13:36:28 +0100 (BST) Received: from astra-cdc-x03.seso.astrazeneca.net (astra-cdc-x03.seso.astrazeneca.net [192.71.145.48]) by sesosn21.seso.astrazeneca.net (8.10.1/8.10.1) with ESMTP id f7ECaRu24637 for ; Tue, 14 Aug 2001 14:36:27 +0200 (MET DST) Received: by astra-cdc-x03.seso.astrazeneca.net with Internet Mail Service (5.5.2650.21) id ; Tue, 14 Aug 2001 14:36:27 +0200 Message-ID: To: chemistry@ccl.net Subject: QSAR Date: Tue, 14 Aug 2001 14:44:29 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-Type: text/plain; charset="iso-8859-1" Dear CCLers: I would appreciate how do you calculate the electronic Hammett constant (Sigma) and lipophilicity parameter (Phi). Can this descriptors are calculable in Cerius2. If yes, please outline the method. Thanks in advance. With Regards S Parthiban From chemistry-request@server.ccl.net Tue Aug 14 12:28:02 2001 Received: from cse.nd.edu (ako@[129.74.25.101]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7EGS2v13466 for ; Tue, 14 Aug 2001 12:28:02 -0400 Received: from localhost (ako@localhost) by cse.nd.edu (8.11.2/8.11.2) with ESMTP id f7EGRw107213 for ; Tue, 14 Aug 2001 11:27:59 -0500 (EST) Date: Tue, 14 Aug 2001 11:27:58 -0500 (EST) From: Alice NgarKit Ko To: chemistry@ccl.net Subject: CHARMM solvation Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone have any generic solvation.inp for CHARMM? Any tips on how to do solvation with CHARMM is greatly appreciated. Thank you Alice From chemistry-request@server.ccl.net Tue Aug 14 15:11:20 2001 Received: from slam.arl.army.mil ([131.218.32.153]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f7EJBGv16024 for ; Tue, 14 Aug 2001 15:11:19 -0400 Subject: Computational Chemistry GRID Conference To: chemistry@ccl.net From: "Mark Zottola - Contractor" Date: Tue, 14 Aug 2001 15:11:13 -0400 Message-ID: X-MIMETrack: Serialize by Router on slam/arl(Release 5.0.8 |June 18, 2001) at 08/14/2001 03:11:19 PM MIME-Version: 1.0 Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f7EJBKv16027 Computational Chemistry GRID Conference SURA and the University of Kentucky, with support from the Army Research Laboratory are co-sponsoring the Computational Chemistry GRID Conference in October. This conference is designed to build connections between the developments in computational chemistry and the user community, and to provide a "bridge" between various internet protocols that are being used to share information. This is the first Internet conference to use technology to link Mbone and H.323 technologies into a single, distributed environment. The conference, on the cutting edge of both science and internet technology, will center on applications of quantum mechanics, molecular dynamics, solid state chemistry and biochemistry. Leaders of quantum mechanics and molecular simulations will be speaking at this conference, including Dr. Keiji Morokuma (Emory) and Dr. Stephen Harvey (UAB). In addition, developers of some of the most widely used quantum codes have accepted invitations to speak: Dr. M. Frisch, Gaussian, Inc., Dr. Theresa Windus of Pacific Northwest Laboratories (NWChem) and Dr. P. Bartlett of the University of Florida (ACES II). This conference will be held October 16th and 17th at the University of Kentucky, Lexington, Kentucky. Talks from invited speakers will address the applications of techniques to research problems and the use of various state-of-the-art packages. Both morning and afternoon sessions will be interactive, allowing remote attendees the opportunity to interact with the speakers via the internet. This conference will also have a web site for those who wish to submit a poster or paper. Registration and further information may be found at: http://www.sura.org/workshops The noteworthy addition to this conference is a technical effort to span the gulf between ACCESS Grid users and H.323 users. Previously, these two collaborative tools have been technologically incompatible, leading to a sharp economic divide between Internet users who had substantial resources (to procure and run an Access Grid node) and those who had more meager resources or needed to focus their resources on a commercially interoperable technology (H.323 users). This conference will showcase a gateway between the Access Grid and H.323, enabling diverse remote conference participation and illuminating a path for less resource rich institutions, such as HBCU's and MSI's to more fully participate in state-of-the-art collaborative environments that are emerging on the Internet for research and education. This Conference is supported by SURA, under a grant from the National Computational Science Alliance (NCSA), serving as a Partner for Advanced Computational Services (PACS). From chemistry-request@server.ccl.net Tue Aug 14 17:56:55 2001 Received: from mc.edu ([204.198.21.52]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f7ELusv18582 for ; Tue, 14 Aug 2001 17:56:55 -0400 Received: from MC-Message_Server by mc.edu with Novell_GroupWise; Tue, 14 Aug 2001 16:56:45 -0500 Message-Id: X-Mailer: Novell GroupWise Internet Agent 5.5.5.1 Date: Tue, 14 Aug 2001 16:56:20 -0500 From: "David Magers" To: Subject: reported decimal accuracy in cartesian displacement vectors in G98 Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f7ELutv18583 Greetings, I apologize if this question has been asked before. I have the vague recollection that it has, but I could find nothing when I searched the CCL database. Anyway, in Gaussian 98, under each frequency, Cartesian displacement vectors are reported for each atom, but they are only reported to two places after the decimal. Is there anyway to increase the reported accuracy of these numbers? I assume I can always convert the checkpoint file to a formatted file, read the force constant matrix myself, and calculate these vectors with better accuracy, but it would be nice if Gaussian would do it for me. Any hints would be most appreciated. Thanks, David ------------------------------------------------------------------------------------- David H. Magers, Ph.D. phone:601-925-3851 Mississippi College fax: 601-925-3933 Professor e-mail: magers@mc.edu Department of Chemistry and Biochemistry Box 4036 Clinton, MS 39058